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|| -flag3 arg3 || brief description ||detailed description (eg, help file information) || || -flag4 arg4 || brief description ||detailed description (eg, help file information) || |
||-mapanalysis|| ||analysisname|| ||get map/contrast from this analysis|| ||-thmin|| ||thresh || ||minimum threshold for display (2)|| ||-thmax|| ||thresh || ||maximum threshold for display (7)|| ||-thmask|| || || ||set thmin = .5 and thmax = 1 (good for masks)|| ||-nohdr|| || || ||do not load/show hemodynamic response|| ||-nosig|| || || ||do not load/show significance map|| ||-raw|| ||run || ||display raw MR from run|| ||-rawstem|| ||stem || ||display raw MR from run/stem|| ||-motioncor|| || || ||display motion corrected raw data (with -raw)|| ||-base|| ||volume || ||t2epi, t1epi, t2conv|| ||-mask|| ||maskid || ||mask using FSD/masks/maskid|| ||-subject|| ||subjectname || ||display on subject's talairached anatomical.only with -space tal; spec -base bshortBI where B = tal res, and I is 1, 2, or 4 || |
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command foo -i f -o out | |
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description |
Index TableOfContents
Name
sliceview-sess - the results are viewed on 2D slices of the brain
Synopsis
sliceview-sess -slice <slicenumber> -analysis <analysis name> -contrast <contrast name> -map <map name> -sf <sessidfile> -sf <sesssirfile>
Arguments
Positional Arguments
Required Flagged Arguments
-slice |
slicenumber |
number of the slice to view |
-analysis |
analysisname |
name of analysis (from mkanalysis-sess) |
-contrast |
contrastname |
name of contrast (from mkcontrast-sess) |
-map |
mapname |
name of map produced by stxgrinder-sess (sig, t, minsig, iminsig) |
-sf |
sessidfile |
see above |
-df |
sessdirfile |
see above |
Optional Flagged Arguments
-mapanalysis |
|
analysisname |
|
get map/contrast from this analysis |
-thmin |
|
thresh |
|
minimum threshold for display (2) |
-thmax |
|
thresh |
|
maximum threshold for display (7) |
-thmask |
|
|
|
set thmin = .5 and thmax = 1 (good for masks) |
-nohdr |
|
|
|
do not load/show hemodynamic response |
-nosig |
|
|
|
do not load/show significance map |
-raw |
|
run |
|
display raw MR from run |
-rawstem |
|
stem |
|
display raw MR from run/stem |
-motioncor |
|
|
|
display motion corrected raw data (with -raw) |
-base |
|
volume |
|
t2epi, t1epi, t2conv |
-mask |
|
maskid |
|
mask using FSD/masks/maskid |
-subject |
|
subjectname |
|
display on subject's talairached anatomical.only with -space tal; spec -base bshortBI where B = tal res, and I is 1, 2, or 4 |
Outputs
No output files are created. When you run sliceview, the functional results are displayed on 2D slices of the brain. You can scroll through different timepoints by using the -/+ keys. To view the hemodynamic response for a particular voxel, click on that voxel and type g.
Description
In Slice-based visualization, the results are viewed on 2D slices of the brain (either individual slices or mosaics of slices). No information about the volume is available. The slices are defined as those in the native functional space. Typically, a significance map from a particular contrast is thresholded and laid over a structural slice. Additionally, for event-related studies the hemodynamic response for each condition can be viewed by clicking on a particular voxel in the slice. To see the individual results for all subjects for a single slice, run sliceview-sess from the Study Directory with the following options.
The results for each subject will be displayed sequentially (ie, you must close the window for one subject before you can see the next). The T1 EPI image as the underlay. If the T1 does not exist, it will use mean functional image as the underlay. For event-related studies, the hemodynamic responses will be automatically loaded. See Appendix A for more details on how to operate the viewer.
Examples
Example 1
Example 2
command foo -i f -o out -f fvalue
description
Bugs
None
See Also
["othercommand1"], ["othercommand2"]
Links
Methods Description
description description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>